Nute Gunray is the Viceroy of the Trade Federation and the leader of the droid army occupying Naboo. He shares antagonist duties with Darth Sidious: he stands in direct conflict with the story's heroes and is the one who must be defeated to bring the conflict to resolution.
Yep, sounds like an antagonist to us.
His motivations also recruit him for Team Villain. His invasion of Naboo stems from pure greed: he doesn't want to pay space taxes—although, to be fair, for all we know those import dues can be killer high. This is the opposite of the heroes' motivations, which originate from a desire to help others.
While these characteristics certainly make him an antagonist, he isn't the antagonist. That title goes to Darth Sidious. Instead, the weak-willed Gunray is more of a tool Sidious is using in a much larger conflict. Consider the first scene between the two:
SIDIOUS: This turn of events is unfortunate. We must accelerate our plans. Begin landing your troops.
GUNRAY: My lord, is that legal?
SIDIOUS: I will make it legal.
GURAY: And the Jedi?
SIDIOUS: The chancellor should never have brought them into this. Kill them immediately.
Clearly Sidious is the one wearing the, erm, robes in this relationship. Gunray is just along for the ride, and doesn't make any decisions on his own. This is typical in all of their conversations: Gunray provides Sidious with an update to the situation, Sidious tells Gunray what to do, and Gunray does it.
The viceroy clearly has misgivings as the situation progresses and escalates well beyond his comfort zone:
GUNRAY: This is getting out of hand. Now there are two [Sith lords].
HAAKO: We should not have made this bargain.
But ol' Nute seems to think things will break his way right until the end. He never realizes that Darth Sidious is using him as a patsy, someone to draw attention away from the Sith's true goals and the greater conflict brewing beneath the Naboo invasion.
And judging by him siding with Count Dooku in Attack of the Clones, he won't be figuring it out anytime soon. Not the brightest Viceroy in the electorate, is he?
Oh, and one more thing: Lucas has come under fire for portraying Gunray in a way that people have likened to an Asian stereotype. Their accents confuse the "r" and "l" sounds in English, and they wear suspiciously Asiatic headdresses. (Source)